Minali, who turned professional only last year, stormed home in five hours five minutes 24 seconds. Germany's Steffen Wessemann was second and Italian sprinter Adriano Baffi third, giving him the overall lead.
Catalan Melchor Mauri, one of the race favorites, built a lead of 12 seconds at one point, but the main field never lost touch and soon swallowed him up again.
Wednesday's 191-kilometer stage runs from Segura Viudas to Altao de la Rabassa in the principality of Andorra.
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